John N Nkengasong

Centers for Disease Control and Prevention, Atlanta, Michigan, United States

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Publications (165)761.43 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Fourth-generation HIV rapid tests (RTs) claim to detect both p24 antigen (Ag) and HIV antibodies (Ab) for early identification of acute infections, important for targeted prevention and reducing HIV transmission. In a nationally representative household survey in Swaziland, 18,172 adults, age 18-49 years, received home-based HIV rapid testing in 2010-2011. Of the 18,172 individuals, 5,822 (32.0%) were Ab+ by Determine HIV-1/2 Ab/Ab Combo and of those, 5,789 (99.4%) were confirmed reactive by Uni-Gold. Determine Combo identified 12 individuals as acute infections (Ag+/Ab-); however, none had detectable HIV-1 RNA and 8 of 12 remained HIV negative at 6-week follow-up visits (4 lost to follow up). All RT non-reactive samples were pooled and tested by nucleic acid amplification testing (NAAT) to identify acute infections. NAAT identified 13 (0.1%) of the 12,338 HIV antibody-negative specimens as HIV RNA positive with RNA levels ranging from 300 to >10,000,000 copies/mL. However, none of them were Ag+ on Determine Combo. Follow-up testing of 12 of the 13 NAAT-positive individuals at 6 months demonstrated 12 seroconversions (1 lost to follow-up). Therefore, the Combo test had a sensitivity of 0% (95% CI 0%-28%) and positive predictive value of 0% for the detection of acute infections. The ability of Determine 4(th) Generation Combo to detect antigen was very poor in Swaziland. Thus, Determine Combo does not add any value to the current testing algorithm; rather it adds additional costs and complexity to HIV diagnosis. The detection of acute HIV infections may need to rely on other testing strategies.
    Journal of clinical microbiology. 08/2014;
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    ABSTRACT: Abstract Strong laboratory services and systems are critical for delivering timely and quality health services that are vital to reduce patient attrition in the HIV treatment and prevention cascade. However, challenges exist in ensuring effective laboratory health systems strengthening and linkages. In particular, linkages and referrals between laboratory testing and other services need to be considered in the context of an integrated health system that includes prevention, treatment, and strategic information. Key components of laboratory health systems that are essential for effective linkages include an adequate workforce, appropriate point-of-care (POC) technology, available financing, supply chain management systems, and quality systems improvement, including accreditation. In this review, we highlight weaknesses of and gaps between laboratory testing and other program services. We propose a model for strengthening these systems to ensure effective linkages of laboratory services for improved access and retention in care of HIV/AIDS patients, particularly in low- and middle-income countries.
    AIDS patient care and STDs 04/2014; · 2.68 Impact Factor
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    ABSTRACT: A voluntary, cost-free external quality assessment (EQA) program established by the U.S. Centers for Disease Control and Prevention (CDC) was implemented to primarily monitor the performance of laboratories conducting HIV Early Infant Diagnosis (EID) from dried blood spots (DBS) in low to middle-income countries since 2006. Ten blinded DBS proficiency test (PT) specimens and 100 known HIV-positive and negative DBS specimens (to be used as internal controls) were shipped tri-annually to participating laboratories with reports for the PT specimens due within 30 days. The participant's results and summary of the performance of all participating laboratories and each diagnostic method were provided after each test cycle. Enrollment in the CDC PT program expanded progressively from 17 laboratories from 11 countries in 2006 to include 136 laboratories from 41 countries at the end of 2012. Despite external pressures to test and treat more children while expanding EID programs, mean PT test scores significantly improved over time as demonstrated by the upward trend from mid-2006 to end of 2012 (P = 0.001) and increase in the percentage of laboratories scoring 100% (P =0.003). The mean test scores plateaued over the past 10 testing cycles, ranging between 98.2 and 99.7% and discordant test results still occur, but at a rate no higher than 2.6%. Analysis of these test results suggests a positive impact of proficiency testing on the testing performance of the participating laboratories and a continuous training program and proficiency testing participation may translate into laboratories improving their testing accuracy.
    Journal of clinical microbiology 12/2013; · 4.16 Impact Factor
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    ABSTRACT: High-throughput, sensitive and cost-effective HIV drug resistance (HIVDR) detection assays are needed for large-scale monitoring of the emergence and transmission of HIVDR in resource-limited settings. Using suspension array technology, we have developed a multiplex allele-specific (MAS) assay that can simultaneously detect major HIVDR mutations at 20 loci. Forty-five allele-specific primers tagged with unique 24-base oligonucleotide at the 5' end were designed to detect wild-type and mutant alleles at the 20 loci of HIV-1 subtype-C viruses. The MAS assay was first established and optimized with three plasmid templates (C-wt, C-mut1 and C-mut2), and then evaluated using 148 plasma specimens from HIV-1 subtype-C-infected individuals. All the wild-type and mutant alleles could be unequivocally distinguished with plasmid templates, and the limits of detection were 1.56% for K219Q and K219E; 3.13% for L76V; 6.25% for K65R, K70R, L74V, L100I, K103N, K103R, Q151M, Y181C and I47V; and 12.5% for M41L, K101P, K101E, V106A, V106M, Y115F, M184V, Y188L, G190A, V32I, I47A, I84V and L90M. Analyses of 148 plasma specimens revealed that MAS assay gave 100% concordance with conventional sequencing at eight loci, and over 95% (95.21%-99.32%) concordance at the remaining 12 loci. The differences observed were mainly caused by 24 additional low-abundance alleles detected by the MAS assay. Ultra-deep sequencing analysis confirmed 15 of 16 low-abundance alleles. The multiplex, sensitive and straightforward result reporting assay represents a new efficient genotyping tool for HIVDR surveillance and monitoring.
    Journal of clinical microbiology 08/2013; · 4.16 Impact Factor
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    ABSTRACT: Abstract Whatman 903 filter paper is the only filter paper that has been used for HIV drug resistance (HIVDR) genotyping in resource-limited settings. In this study, we evaluated another dried blood specimen collection device, termed SampleTanker(®) (ST), for HIVDR genotyping. Blood specimens from 123 antiretroviral therapy (ART)-experienced patients were used to prepare ST whole blood and ST plasma specimens; they were then stored at ambient temperature for 2 or 4 weeks. The remaining plasma specimens were stored at -80°C and used as frozen plasma controls. Frozen plasma viral load (VL) was determined using the Roche Amplicor HIV-1 Monitor test, v.1.5 and 50 specimens with VL ≥3.00 log10 copies/ml were genotyped using the broadly sensitive genotyping assay. The medium VL for the 50 frozen plasma specimens with VL ≥3.00 log10 was 3.58 log10 copies/ml (IQR: 3.32-4.11) and 96.0% (48/50) of them were genotyped. Comparing to frozen plasma specimens, significantly lower genotyping rates were obtained from ST whole blood (48.98% and 42.85%) and ST plasma specimens (36.0% and 36.0%) stored at ambient temperature for 2 and 4 weeks, respectively (p<0.001). Nucleotide sequence identity and resistance profile analyses between the matched frozen plasma and ST whole blood or ST plasma specimens revealed high nucleotide sequence identities and concordant resistance profiles (98.1% and 99.0%, and 96.6% and 98.9%, respectively). Our results indicate that with the current design, the ST may not be the ideal dried blood specimen collection device for HIVDR monitoring for ART patients in resource-limited settings.
    AIDS research and human retroviruses 08/2013; · 2.18 Impact Factor
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    ABSTRACT: Laboratory systems worldwide are challenged not only by the need to compete for scarce resources with other sections of national health care programmes, but also with the lack of understanding of the critical role that laboratories play in the accurate diagnosis and monitoring of patients suffering from high-burdens of disease. An effective approach to establishing cost-effective laboratory systems that provide rapid and accurate test results for optimal impact on patient care is to move away from disease-specific programmes and establish integrated laboratory services. An integrated laboratory network provides all primary diagnostic services needed for care and treatment without requiring patients to go to different laboratory facilities for specific tests. Such a network focuses on providing quality-assured basic laboratory testing through the use of common specimen collection, reporting and diagnostic platforms that can be used across diseases. An integrated laboratory system also provides specimen transport to specialised laboratories and an environment conducive to the introduction and use of new and more complex technologies that would benefit the patient population and public health systems as a whole. As such, this article described various strategies for, and practical examples of, the successful integration of laboratory services.
    African Journal of Laboratory Medicine. 04/2013;
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    ABSTRACT: In Kenya, HIV-1 viral load monitoring is commonly performed with the Cobas Amplicor using plasma specimens. Interest is growing in transitioning to real-time PCR (RT-PCR), such as the Cobas Ampliprep/Cobas TaqMan (CAP/CTM), using dried blood spots (DBS). Before implementation, direct evaluation of the two assays using DBS field specimens is required. This study compares the sensitivity, specificity, negative and positive predictive values (NPV and PPV, respectively), concordance, and agreement between HIV-1 viral load measurements using plasma and DBS specimens obtained from 512 HIV-1-infected pregnant females enrolled in the Kisumu Breastfeeding Study and tested with the Cobas Amplicor and CAP/CTM assays. The sensitivity and NPV of viral load detection in DBS specimens were higher with CAP/CTM (sensitivity, 100%; 95% confidence interval [CI], 99.1 to 100.0%; NPV, 100%; 95% CI, 59.0 to 100.0%) than the Cobas Amplicor (sensitivity, 96.6%; 95% CI, 94.3 to 98.1%; NPV, 58.8%; 95% CI, 40.7 to 75.4%). The PPVs were comparable between both assays when using DBS. The specificity of viral load detection in DBS specimens was lower with CAP/CTM (77.8%; 95% CI, 40.0 to 97.2%) than that of the Cobas Amplicor (95.2%; 95% CI, 76.2 to 99.9%). Good concordance and agreement were observed when paired plasma and DBS specimens were tested with both assays. Lower specificity with the CAP/CTM is likely due to proviral HIV-1 DNA amplification and lower detection limits with RT-PCR. However, the CAP/CTM has better sensitivity and higher throughput than the Cobas Amplicor. These findings suggest that DBS may be a suitable alternative to plasma when using RT-PCR, which could increase access to viral load monitoring in resource-limited settings.
    Journal of clinical microbiology 04/2013; 6(51):1208-18. · 4.16 Impact Factor
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    ABSTRACT: In Kenya, HIV-1 viral load monitoring is commonly performed with the Cobas Amplicor using plasma specimens. Interest is growing in transitioning to real-time PCR (RT-PCR), such as the Cobas Ampliprep/Cobas TaqMan (CAP/CTM), using dried blood spots (DBS). Before implementation, direct evaluation of the two assays using DBS field specimens is required. This study compares the sensitivity, specificity, negative and positive predictive values (NPV and PPV, respectively), concordance, and agreement between HIV-1 viral load measurements using plasma and DBS specimens obtained from 512 HIV-1-infected pregnant females enrolled in the Kisumu Breastfeeding Study and tested with the Cobas Amplicor and CAP/CTM assays. The sensitivity and NPV of viral load detection in DBS specimens were higher with CAP/CTM (sensitivity, 100%; 95% confidence interval [CI], 99.1 to 100.0%; NPV, 100%; 95% CI, 59.0 to 100.0%) than the Cobas Amplicor (sensitivity, 96.6%; 95% CI, 94.3 to 98.1%; NPV, 58.8%; 95% CI, 40.7 to 75.4%). The PPVs were comparable between both assays when using DBS. The specificity of viral load detection in DBS specimens was lower with CAP/CTM (77.8%; 95% CI, 40.0 to 97.2%) than that of the Cobas Amplicor (95.2%; 95% CI, 76.2 to 99.9%). Good concordance and agreement were observed when paired plasma and DBS specimens were tested with both assays. Lower specificity with the CAP/CTM is likely due to proviral HIV-1 DNA amplification and lower detection limits with RT-PCR. However, the CAP/CTM has better sensitivity and higher throughput than the Cobas Amplicor. These findings suggest that DBS may be a suitable alternative to plasma when using RT-PCR, which could increase access to viral load monitoring in resource-limited settings.
    Journal of Clinical Microbiology. 04/2013; 51(4).
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    ABSTRACT: In Kenya, HIV-1 viral load monitoring is commonly performed with the COBAS Amplicor using plasma specimens. Interest is growing in transitioning to real-time PCR (RT-PCR), such as the COBAS Ampliprep/COBAS Taqman (CAP/CTM), using dried blood spots (DBS). Before implementation, direct evaluation of the two assays using DBS field specimens is required. This study compares sensitivity, specificity, negative (NPV) and positive (PPV) predictive values, concordance, and agreement between HIV-1 viral load measurements using plasma and DBS specimens obtained from 512 HIV-1 infected pregnant females enrolled in the Kisumu Breastfeeding Study, and tested with the COBAS Amplicor and CAP/CTM assays. The sensitivity and NPV of viral load detection in DBS specimens were higher with CAP/CTM (sensitivity: 100%, 95% CI: 99.1-100.0; NPV: 100%, 95% CI: 59.0-100.0%) than the COBAS Amplicor (sensitivity: 96.6%, 95% CI: 94.3-98.1; NPV: 58.8%, 95% CI: 40.7-75.4). PPV was comparable between both assays when using DBS. The specificity of viral load detection in DBS specimens was lower with CAP/CTM (77.8%, 95% CI: 40.0-97.2) than the COBAS Amplicor (95.2%, 95% CI: 76.2-99.9). Good concordance and agreement were observed when testing paired plasma and DBS specimens with both assays. Lower specificity with the CAP/CTM is likely due to pro-viral HIV-1 DNA amplification and lower detection limits with RT-PCR. However, the CAP/CTM has better sensitivity and higher throughput when compared with the COBAS Amplicor. These findings suggest that DBS may be a suitable alternative to plasma when using RT-PCR, which could increase access to viral load monitoring in resource limited settings.
    Journal of clinical microbiology 02/2013; · 4.16 Impact Factor
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    ABSTRACT: Detection of recent HIV infections is a prerequisite for reliable estimations of transmitted HIV drug resistance (t-HIVDR) and incidence. However, accurately identifying recent HIV infection is challenging due partially to the limitations of current serological tests. Ambiguous nucleotides are newly emerged mutations in quasispecies, and accumulate by time of viral infection. We utilized ambiguous mutations to establish a measurement for detecting recent HIV infection and monitoring early HIVDR development. Ambiguous nucleotides were extracted from HIV-1 pol-gene sequences in the datasets of recent (HIVDR threshold surveys [HIVDR-TS] in 7 countries; n=416) and established infections (1 HIVDR monitoring survey at baseline; n=271). An ambiguous mutation index of 2.04×10(-3) nts/site was detected in HIV-1 recent infections which is equivalent to the HIV-1 substitution rate (2×10(-3) nts/site/year) reported before. However, significantly higher index (14.41×10(-3) nts/site) was revealed with established infections. Using this substitution rate, 75.2% subjects in HIVDR-TS with the exception of the Vietnam dataset and 3.3% those in HIVDR-baseline were classified as recent infection within one year. We also calculated mutation scores at amino acid level at HIVDR sites based on ambiguous or fitted mutations. The overall mutation scores caused by ambiguous mutations increased (0.54×10(-2)3.48×10(-2)/DR-site) whereas those caused by fitted mutations remained stable (7.50-7.89×10(-2)/DR-site) in both recent and established infections, indicating that t-HIVDR exists in drug-naïve populations regardless of infection status in which new HIVDR continues to emerge. Our findings suggest that characterization of ambiguous mutations in HIV may serve as an additional tool to differentiate recent from established infections and to monitor HIVDR emergence.
    PLoS ONE 01/2013; 8(10):e77649. · 3.53 Impact Factor
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    ABSTRACT: Participation in external quality assessment programs is critical to ensure quality clinical laboratory testing. Commercially available proficiency test panels for HIV-1 virus load testing that are used commonly in external quality assessment programs remain a financial obstacle to resource-limited countries. Maintaining cold-chain transportation largely contributes to the cost of traditional liquid proficiency test panels. Therefore, we developed and evaluated a proficiency test panel using dried tube specimens that can be shipped and stored at ambient temperature. This dried tube specimens panel consisted of 20μl aliquots of a HIV-1 stock that were added to 2ml tubes and left uncapped for drying, as a preservation method. The stability of dried tube specimens at concentrations ranging from 10(2) to 10(6.5) RNA copies/ml was tested at different temperatures over time, showing no viral load reduction at 37°C and a decrease in viral load smaller than 0.5 Log(10) at 45°C for up to eight weeks when compared to initial results. Eight cycles of freezing-thawing had no effect on the stability of the dried tube specimens. Comparable viral load results were observed when dried tube specimen panels were tested on Roche CAPTAQ, Abbott m2000, and Biomerieux easyMAG viral load systems. Preliminary test results of dried proficiency test panels shipped to four African countries at ambient temperature demonstrated a low inter assay variation (SD range: 0.29-0.41 Log(10) RNA copies/ml). These results indicated that HIV-1 proficiency test panels generated by this methodology might be an acceptable alternative for laboratories in resource-limited countries to participate in external quality assessment programs.
    Journal of virological methods 12/2012; · 2.13 Impact Factor
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    ABSTRACT: HIV-1 drug resistance (HIVDR) assays are important tools in clinical management of HIV-infected patients on antiretroviral therapy (ART) and surveillance of drug resistant variants at population levels. The high cost associated with commercial assays hinders their use in resource-limited settings. We adopted and validated a low cost in-house assay using 68 matched plasma and dried blood spot (DBS) samples with a median viral load (VL) of 58,187copies/ml, ranging from 253 to 3,264,850 against the commercial assay ViroSeq. Results indicated that the in-house assay not only had higher plasma genotyping rate than ViroSeq (94% vs. 78%), but also was able to genotype 89.5% (51/57) of the matched DBS samples with VLs of ≥1,000 copies/ml. The sensitivity in detecting DR mutations by the in-house assay was 98.29% (95% CI: 97.86-98.72) on plasma and 96.54 (95% CI: 95.93-97.15) on DBS and the specificity was 99.97% (95% CI: 99.91-100.00) for both sample types when compared to ViroSeq. The minor DR mutation differences detected by the in-house assay against the Viroseq didn't result in the clinical significance. In addition, cost analysis showed that the in-house assay could reduce the genotyping cost by about 60% for both plasma and DBS comparing to ViroSeq.This field condition evaluation highlights the potential utility of a cost-effective, subtype-independent in-house genotyping assay using both plasma and DBS specimens for HIVDR clinical monitoring and population based surveillance in resource-limited settings.
    Journal of clinical microbiology 12/2012; · 4.16 Impact Factor
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    ABSTRACT: Background: Dried blood spots (DBS) collected on filter paper have eased the difficulty of blood collection in resource-limited settings. Currently Whatman 903 (W-903) is the only filter paper that has been used for HIV viral load (VL) and HIV drug resistance (HIVDR) testing. We therefore evaluated two additional commercially available filter papers, Ahlstrom grade 226 (A-226) and Munktell TFN (M-TFN) for VL and HIVDR genotyping using W-903 as a comparison group.Methods: DBS specimens were generated from 344 adult ART-patients in Botswana. VL was measured with NucliSENS EasyQ HIV-1 v2.0 and genotyping was performed for those specimens with a detectable VL (≥ 2.90 log10 copies/ml) using an in-house method.Results: Bland-Altman analysis revealed strong concordance in quantitative VL analysis between W-903 and A-226 (bias= -0.034 ± 0.246 log10 copies/ml [Mean difference ± SD]) and M-TFN (bias = -0.028± 0.186 log10 copies/ml) while qualitative VL analysis for virological failure determination, defined as VL ≥ 3.00 log10 copies/ml, showed low sensitivities for A-266 (71.54%) and M-TFN (65.71%) when compared to W-903. DBS collected on M-TFN had the highest genotyping efficiency (100%) compared to W-903 and A-226 (91.7%), and appear more sensitive in detecting major HIVDR mutations.Conclusions: DBS collected on A-226 and M-TFN filter papers performed similarly to W-903 for quantitative VL analysis and HIVDR detection. Together, the encouraging genotyping results and the variability observed in determining virological failure from this small pilot study warrant further investigation of A-226 and M-TFN as specimen collection devices for HIVDR monitoring surveys.
    Journal of clinical microbiology 10/2012; · 4.16 Impact Factor
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    ABSTRACT: Abstract Shandong province has been providing antiretroviral therapy (ART) to eligible HIV/AIDS patients since 2003 using first-line regimens. We conducted a cross-sectional study to assess virological response and resistance development from ART patients. Between 2006 and 2008, blood was collected from 143 ART patients. Viral load (VL) was determined with a detection limit of 50 copies/ml; those with detectable VL were genotyped with dried plasma spots using a broadly sensitive genotyping assay. Resistance mutations were identified using the Stanford HIV drug resistance database. Of the 143 patients, 72% [95% confidence interval (CI): 65.9-78.2] suppressed their VL to <50 copies/ml. Genotyping analysis of the remaining 40 patients revealed that 21 (53%, CI: 37.0-68.0) harbored one or more mutations. The most common mutations were thymidine-analog mutations (22.5%) and M184V (10%) to nucleoside reverse transcriptase inhibitors (NRTIs), and V106I/A /M (17.5%), Y181C (15%), and H221Y (12.5%) to non-NRTIs (NNRTIs); 13 patients had mutations to both NRTIs and NNRTIs. Patients with VL >1000 copies/ml appear to harbor more mutations than those with VL between 50 and 1000 (62.1% vs. 27.3%, p>0.05). Resistance mutations were intensified among 10 patients for whom two sequential specimens were obtained and accumulation of resistance mutations predicted compromised treatment outcomes and future drug selections. This study provides a snapshot of the virological responses and resistance profiles for patients on first-line regimens, indicating that patient monitoring is a critical component in preventing the accumulation of resistance mutations among patients failing their regimens and thus maintaining the effectiveness of the first-line regimens.
    AIDS research and human retroviruses 05/2012; · 2.18 Impact Factor
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    ABSTRACT: The President's Emergency Plan for AIDS Relief (PEPFAR) programme for the Caribbean Region was established in 2008 to address health system challenges, including fragile laboratory services and systems. The laboratory component of this programme consisted of several phases: assessment of laboratory needs of all 12 countries engaged in the programme; addressing gaps identified during the assessment; and monitoring and evaluation of the progress achieved. After one year of PEPFAR collaboration with national governments and other partners, laboratory services and systems greatly improved. Some of the milestones include: (1) the accreditation of a public laboratory; (2) improved access to HIV diagnosis with faster turnaround time; (3) establishment of capacity for platforms for DNA PCR, viral load and HIV drug resistance; (4) development of the laboratory workforce; and (5) establishment of a framework for implementation of sustainable quality management systems for laboratory accreditation. The progress recorded in strengthening laboratory health systems after one year of initiating this collaboration shows that with a rigorous initial assessment, programme design and intervention and strategic partnership, national laboratory health systems can be greatly enhanced to support programme implementation. Continued collaboration and country leadership is critical to create an integrated and sustainable laboratory network in the Caribbean.
    Global Public Health 04/2012; 7(6):648-60. · 0.92 Impact Factor
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    ABSTRACT: Antiretroviral therapy (ART) is being administered in developing nations at unprecedented numbers following the World Health Organization's (WHO) development of standardized first-line drug regimens. To ensure continued efficacy of these drug regimens, WHO recommends monitoring virological responses and development of human immunodeficiency virus (HIV) drug resistance (HIVDR) in HIV-infected patients in a prospective cohort. The current study compared dried fluid spot specimens with the reference standard plasma specimens as a practical tool for viral load (VL) and HIVDR genotyping in resource-limited settings. Dried blood spot (DBS), dried plasma spot (DPS), and plasma specimens were collected from 173 -patients receiving ART at 2 hospital sites in Abuja, Nigeria. HIV-1 VL analysis was performed using NucliSENS EasyQ HIV-1 v1.1 RUO test kits. Genotyping of the HIV-1 pol gene was performed using a broadly sensitive in-house assay. Direct comparison of VL levels showed that DBS specimens, and not DPS specimens, gave results comparable to those of plasma specimens (P = .0619 and .0007, respectively); however, both DBS and DPS specimens had excellent correlation with plasma specimens in predicting virological failure (VL, ≥1000 copies/mL) in patients (κ = 0.78 and 0.83, respectively). Of the 18 specimens with a plasma VL ≥1000 copies/mL, HIVDR genotyping rates were 100% in DBS and 38.9% in DPS specimens, and DBS specimens identified 61 of 65 HIVDR mutations (93.8%) identified in plasma specimens. Our results indicate that DBS specimens could be used for surveys to monitor HIVDR prevention failure in resource-limited settings.
    Clinical Infectious Diseases 03/2012; 54(8):1187-95. · 9.37 Impact Factor
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    Advances in experimental medicine and biology 01/2012; 743:51-65. · 1.83 Impact Factor
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    ABSTRACT: The World Health Organization currently does not recommend the use of dried blood spot specimens for drug resistance testing in patients undergoing antiretroviral therapy (ART). Therefore, HIV-1 resistance testing using peripheral blood mononuclear cells (PBMCs) may be of value in resource-limited settings. We compared genotypic resistance profiles in plasma and PBMCs from patients failing ART in two cities of Honduras (Tegucigalpa and San Pedro Sula), a resource-limited country. One hundred patients failing ART were randomly selected from a longitudinal patient monitoring cohort. Plasma and PBMC samples without patient identifier were used for genotypic resistance testing. Sequence data were analyzed, resistance profiles were determined and compared using Stanford HIV Drug Resistance Database algorithm. Specimens with concordant resistance profiles between the two compartments were 88% (95% CI: 80.3% - 94.5 %). Nine specimens (12%, 95% CI: 6.5% - 21.3%) had discordant resistance profiles of clinical significance. Logistic regression analyses indicated that patients on triple therapy were 17.24 times more likely to have concordant drug resistance profile than those on non-triple therapies (OR=17.24, 95% CI: 3.48, 83.33), while patients with increasing number of regimens and years on ART have a decreased rate of concordance (OR = 0.59, 95% CI: 0.32, 1.09 and OR = 0.62, 95% CI: 0.43, 0.88), respectively, than those with less number of regimens and years on ART. Our results show high level of concordance between plasma and PBMC resistance profiles, indicating the possibility of using PBMCs for drug resistance testing in resources-limited settings.
    International Journal of Molecular Epidemiology and Genetics 01/2012; 3(1):56-65.
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    ABSTRACT: Accurate and reliable laboratory methods are needed for estimation of HIV-1 incidence to identify the high-risk populations and target and monitor prevention efforts. We previously described a single-well limiting-antigen avidity enzyme immunoassay (LAg-Avidity EIA) to detect recent HIV-1 infection. We describe here further optimization and characterization of LAg-Avidity EIA, comparing it to the BED assay and a two-well avidity-index (AI) EIA. Specimen sets included longitudinal sera (n = 393), collected from 89 seroconverting individuals from 4 cohorts representing 4 HIV-1 subtypes, and sera from AIDS patients (n = 488) with or without TB co-infections from 3 different cohorts. Ninety seven HIV-1 positive specimens were purchased commercially. The BED assay, LAg-Avidity EIA, AI-EIA and HIV serology were performed, as needed. Monitoring quality control specimens indicated high reproducibility of the LAg-Avidity EIA with coefficient of variation of <10% in the dynamic range. The LAg-Avidity EIA has an overall mean duration of recency (ω) of 141 days (95% CI 119-160) at normalized optical density (ODn) cutoff of 1.0, with similar ω in different HIV-1 subtypes and populations (132 to 143 days). Antibody avidity kinetics were similar among individuals and subtypes by both the LAg-Avidity EIA and AI-EIA compared to the HIV-IgG levels measured by the BED assay. The false recent rate among individuals with AIDS was 0.2% with the LAg-Avidity EIA, compared to 2.9% with the BED assay. Western blot profiles of specimens with increasing avidity confirm accurate detection of recent HIV-1 infections. These data demonstrate that the LAg-Avidity EIA is a promising assay with consistent ω in different populations and subtypes. The assay should be very useful for 1) estimating HIV-1 incidence in cross-sectional specimens as part of HIV surveillance, 2) identifying risk factors for recent infections, 3) measuring impact of prevention programs, and 4) studying avidity maturation during vaccine trials.
    PLoS ONE 01/2012; 7(3):e33328. · 3.53 Impact Factor

Publication Stats

3k Citations
761.43 Total Impact Points

Institutions

  • 1999–2014
    • Centers for Disease Control and Prevention
      • • Division of Global HIV/AIDS
      • • Division of HIV/AIDS Prevention, Intervention and Support
      • • Division of HIV/AIDS Prevention, Surveillance and Epidemiology
      • • National Center for Emerging and Zoonotic Infectious Diseases
      Atlanta, Michigan, United States
  • 2012–2013
    • Kenya Medical Research Institute
      • Centre for Global Health Research
      Nairobi, Nairobi Province, Kenya
  • 2010–2011
    • Kenya Centers for Disease Control and Prevention
      Winam, Kisumu, Kenya
    • Ministry of Health, Uganda
      Kampala, Central Region, Uganda
  • 1992–2011
    • Institute Of Tropical Medicine
      Antwerpen, Flanders, Belgium
  • 2009
    • Chinese Center For Disease Control And Prevention
      • National Center for AIDS/STD Control and Prevention
      Beijing, Beijing Shi, China
  • 1999–2009
    • Institut de Recherches Mathematiques , Cote d'Ivoire, Abidjan
      Abijan, Lagunes, Ivory Coast
  • 2008
    • National Health Laboratory Service
      Johannesburg, Gauteng, South Africa
  • 2004
    • National Institute of Allergy and Infectious Diseases
      Maryland, United States
  • 2001
    • Roche
      Bâle, Basel-City, Switzerland
  • 1998–2001
    • Centers for Disease Control, Lesotho
      Maseru, Maseru, Lesotho
  • 2000
    • UNAIDS
      Genève, Geneva, Switzerland